Multiple sequence alignment - TraesCS7A01G081200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G081200 chr7A 100.000 3860 0 0 1 3860 46727563 46723704 0.000000e+00 7129
1 TraesCS7A01G081200 chr7A 97.796 953 11 5 1 944 194170994 194171945 0.000000e+00 1635
2 TraesCS7A01G081200 chr7A 96.222 953 17 5 1 944 98752309 98753251 0.000000e+00 1543
3 TraesCS7A01G081200 chr7A 96.933 489 7 4 469 951 46764561 46764075 0.000000e+00 813
4 TraesCS7A01G081200 chr7D 91.870 2915 155 39 994 3860 44303807 44300927 0.000000e+00 3995
5 TraesCS7A01G081200 chr7D 95.090 774 31 3 21 788 321478407 321479179 0.000000e+00 1212
6 TraesCS7A01G081200 chr7D 94.839 155 8 0 790 944 321479223 321479377 3.850000e-60 243
7 TraesCS7A01G081200 chr4A 94.243 2345 107 13 993 3328 655264202 655261877 0.000000e+00 3557
8 TraesCS7A01G081200 chr4A 84.539 608 70 12 152 741 626532676 626532075 7.190000e-162 580
9 TraesCS7A01G081200 chr4A 79.532 513 61 21 3318 3804 655261824 655261330 3.720000e-85 326
10 TraesCS7A01G081200 chr5A 97.696 955 12 5 1 948 41482597 41481646 0.000000e+00 1633
11 TraesCS7A01G081200 chr5B 84.868 608 68 12 152 741 48320622 48321223 3.320000e-165 592
12 TraesCS7A01G081200 chr5B 84.729 609 68 13 152 741 457388852 457388250 1.550000e-163 586
13 TraesCS7A01G081200 chr5D 84.754 610 64 16 152 741 500934243 500934843 5.560000e-163 584
14 TraesCS7A01G081200 chr1B 84.401 609 70 12 152 741 626237727 626237125 3.340000e-160 575
15 TraesCS7A01G081200 chr1B 98.065 155 3 0 790 944 673721605 673721451 1.770000e-68 270
16 TraesCS7A01G081200 chr1B 88.596 114 11 2 11 123 87742765 87742653 1.870000e-28 137
17 TraesCS7A01G081200 chr6A 93.229 192 7 2 759 944 181904850 181905041 1.060000e-70 278
18 TraesCS7A01G081200 chrUn 97.419 155 4 0 790 944 86827072 86826918 8.220000e-67 265
19 TraesCS7A01G081200 chr2A 84.564 149 16 3 792 940 410272250 410272391 1.450000e-29 141


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G081200 chr7A 46723704 46727563 3859 True 7129.0 7129 100.0000 1 3860 1 chr7A.!!$R1 3859
1 TraesCS7A01G081200 chr7A 194170994 194171945 951 False 1635.0 1635 97.7960 1 944 1 chr7A.!!$F2 943
2 TraesCS7A01G081200 chr7A 98752309 98753251 942 False 1543.0 1543 96.2220 1 944 1 chr7A.!!$F1 943
3 TraesCS7A01G081200 chr7D 44300927 44303807 2880 True 3995.0 3995 91.8700 994 3860 1 chr7D.!!$R1 2866
4 TraesCS7A01G081200 chr7D 321478407 321479377 970 False 727.5 1212 94.9645 21 944 2 chr7D.!!$F1 923
5 TraesCS7A01G081200 chr4A 655261330 655264202 2872 True 1941.5 3557 86.8875 993 3804 2 chr4A.!!$R2 2811
6 TraesCS7A01G081200 chr4A 626532075 626532676 601 True 580.0 580 84.5390 152 741 1 chr4A.!!$R1 589
7 TraesCS7A01G081200 chr5A 41481646 41482597 951 True 1633.0 1633 97.6960 1 948 1 chr5A.!!$R1 947
8 TraesCS7A01G081200 chr5B 48320622 48321223 601 False 592.0 592 84.8680 152 741 1 chr5B.!!$F1 589
9 TraesCS7A01G081200 chr5B 457388250 457388852 602 True 586.0 586 84.7290 152 741 1 chr5B.!!$R1 589
10 TraesCS7A01G081200 chr5D 500934243 500934843 600 False 584.0 584 84.7540 152 741 1 chr5D.!!$F1 589
11 TraesCS7A01G081200 chr1B 626237125 626237727 602 True 575.0 575 84.4010 152 741 1 chr1B.!!$R2 589

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
829 899 1.673665 CCTGGAGAGCCAAGCACAC 60.674 63.158 0.0 0.0 45.41 3.82 F
1722 1801 0.250513 ACCTCAGGATTGACGAAGCC 59.749 55.000 0.0 0.0 37.97 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 2746 0.253044 TCCAACTACATCCTGGCTGC 59.747 55.000 0.0 0.0 0.00 5.25 R
2893 2972 1.135575 GCAAAATGCTTCCCTCTGACG 60.136 52.381 0.0 0.0 40.96 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
390 394 7.168219 TGGTATCATTCTTAGAGCACAAAGTT 58.832 34.615 0.00 0.00 0.00 2.66
449 469 3.610040 TCGCATGATTCTGTGGTTACT 57.390 42.857 0.00 0.00 0.00 2.24
612 634 8.560355 TTAAATTGCTGACTTTGAGCACTATA 57.440 30.769 0.00 0.00 46.06 1.31
742 765 4.260990 CCAATTTGTGTCGAAGTGCAGTTA 60.261 41.667 6.80 0.00 0.00 2.24
765 793 9.855021 GTTATATTGGAAATTGCTTGTGTAGTT 57.145 29.630 0.00 0.00 0.00 2.24
788 816 3.748568 TGTGCTGTTGAATATGCGTGTAA 59.251 39.130 0.00 0.00 0.00 2.41
829 899 1.673665 CCTGGAGAGCCAAGCACAC 60.674 63.158 0.00 0.00 45.41 3.82
944 1014 2.550699 TACATTCCAAGCGGGGCCTG 62.551 60.000 8.39 8.39 37.22 4.85
946 1016 2.917897 ATTCCAAGCGGGGCCTGAA 61.918 57.895 18.84 0.30 37.22 3.02
947 1017 2.843912 ATTCCAAGCGGGGCCTGAAG 62.844 60.000 18.84 4.21 37.22 3.02
963 1033 5.296151 CCTGAAGGCCTAAACATAGATCA 57.704 43.478 5.16 0.97 0.00 2.92
964 1034 5.874093 CCTGAAGGCCTAAACATAGATCAT 58.126 41.667 5.16 0.00 0.00 2.45
965 1035 6.302269 CCTGAAGGCCTAAACATAGATCATT 58.698 40.000 5.16 0.00 0.00 2.57
966 1036 6.429385 CCTGAAGGCCTAAACATAGATCATTC 59.571 42.308 5.16 0.00 0.00 2.67
967 1037 6.299141 TGAAGGCCTAAACATAGATCATTCC 58.701 40.000 5.16 0.00 0.00 3.01
968 1038 5.912149 AGGCCTAAACATAGATCATTCCA 57.088 39.130 1.29 0.00 0.00 3.53
969 1039 6.460103 AGGCCTAAACATAGATCATTCCAT 57.540 37.500 1.29 0.00 0.00 3.41
970 1040 6.856757 AGGCCTAAACATAGATCATTCCATT 58.143 36.000 1.29 0.00 0.00 3.16
971 1041 6.944862 AGGCCTAAACATAGATCATTCCATTC 59.055 38.462 1.29 0.00 0.00 2.67
972 1042 6.716628 GGCCTAAACATAGATCATTCCATTCA 59.283 38.462 0.00 0.00 0.00 2.57
973 1043 7.308830 GGCCTAAACATAGATCATTCCATTCAC 60.309 40.741 0.00 0.00 0.00 3.18
974 1044 7.229306 GCCTAAACATAGATCATTCCATTCACA 59.771 37.037 0.00 0.00 0.00 3.58
975 1045 8.781196 CCTAAACATAGATCATTCCATTCACAG 58.219 37.037 0.00 0.00 0.00 3.66
976 1046 9.551734 CTAAACATAGATCATTCCATTCACAGA 57.448 33.333 0.00 0.00 0.00 3.41
977 1047 7.798596 AACATAGATCATTCCATTCACAGAC 57.201 36.000 0.00 0.00 0.00 3.51
978 1048 7.134362 ACATAGATCATTCCATTCACAGACT 57.866 36.000 0.00 0.00 0.00 3.24
979 1049 7.215789 ACATAGATCATTCCATTCACAGACTC 58.784 38.462 0.00 0.00 0.00 3.36
980 1050 5.954153 AGATCATTCCATTCACAGACTCT 57.046 39.130 0.00 0.00 0.00 3.24
981 1051 5.672503 AGATCATTCCATTCACAGACTCTG 58.327 41.667 4.36 4.36 37.52 3.35
982 1052 4.212143 TCATTCCATTCACAGACTCTGG 57.788 45.455 10.86 0.24 35.51 3.86
983 1053 3.840078 TCATTCCATTCACAGACTCTGGA 59.160 43.478 10.86 2.56 35.51 3.86
984 1054 4.472470 TCATTCCATTCACAGACTCTGGAT 59.528 41.667 10.86 0.00 35.99 3.41
985 1055 4.916041 TTCCATTCACAGACTCTGGATT 57.084 40.909 10.86 0.00 35.99 3.01
986 1056 4.478206 TCCATTCACAGACTCTGGATTC 57.522 45.455 10.86 0.00 35.51 2.52
987 1057 3.840078 TCCATTCACAGACTCTGGATTCA 59.160 43.478 10.86 0.00 35.51 2.57
988 1058 3.937706 CCATTCACAGACTCTGGATTCAC 59.062 47.826 10.86 0.00 35.51 3.18
989 1059 4.564199 CCATTCACAGACTCTGGATTCACA 60.564 45.833 10.86 0.00 35.51 3.58
990 1060 4.897509 TTCACAGACTCTGGATTCACAT 57.102 40.909 10.86 0.00 35.51 3.21
991 1061 4.462508 TCACAGACTCTGGATTCACATC 57.537 45.455 10.86 0.00 35.51 3.06
1007 1077 2.617308 CACATCTTCTAAGCATGGCAGG 59.383 50.000 0.00 0.00 0.00 4.85
1009 1079 2.698855 TCTTCTAAGCATGGCAGGTC 57.301 50.000 0.00 0.00 0.00 3.85
1059 1129 3.059982 CTCCAACTCGCCTCCACA 58.940 61.111 0.00 0.00 0.00 4.17
1072 1142 2.187958 CCTCCACATTCTCCTACCACA 58.812 52.381 0.00 0.00 0.00 4.17
1689 1768 1.422781 TCCTGGAATGCCATGATCTCC 59.577 52.381 0.00 0.00 44.91 3.71
1713 1792 2.998949 GCCCGGAACCTCAGGATT 59.001 61.111 0.73 0.00 33.29 3.01
1722 1801 0.250513 ACCTCAGGATTGACGAAGCC 59.749 55.000 0.00 0.00 37.97 4.35
1773 1852 1.880027 GACGTGGCTTCTTGGAACATT 59.120 47.619 0.00 0.00 39.30 2.71
2075 2154 9.098355 TCAGTTTGATAATTTTATCGAGTCCAG 57.902 33.333 5.98 0.56 41.87 3.86
2076 2155 7.852945 CAGTTTGATAATTTTATCGAGTCCAGC 59.147 37.037 5.98 0.00 41.87 4.85
2348 2427 9.846248 GATATTTGAATACATGGCAAAGGATAC 57.154 33.333 0.00 0.00 35.29 2.24
2517 2596 4.277174 TGTAACGCACATGGAAATGAAAGT 59.723 37.500 0.00 0.00 30.04 2.66
2556 2635 6.370994 CAGCAAGAAATCTCTTAGAAGCAGAA 59.629 38.462 0.00 0.00 40.05 3.02
2580 2659 4.576463 CCTGATAATGCTGGAACTTACACC 59.424 45.833 0.00 0.00 0.00 4.16
2637 2716 3.189287 GGAAAGAAGCAGCAAAGATTCGA 59.811 43.478 0.00 0.00 38.83 3.71
2641 2720 5.016051 AGAAGCAGCAAAGATTCGATCTA 57.984 39.130 0.00 0.00 39.08 1.98
2706 2785 4.207165 GGATTGAGCTGGCAAATAAGGTA 58.793 43.478 0.00 0.00 0.00 3.08
2739 2818 1.227556 ACGTGACAAGTCCCACAGC 60.228 57.895 0.00 0.00 33.13 4.40
2817 2896 1.910722 CAGTGATCCCAGGGACCAG 59.089 63.158 11.70 0.00 32.98 4.00
2822 2901 1.005289 ATCCCAGGGACCAGATGCT 59.995 57.895 11.70 0.00 32.98 3.79
2841 2920 6.441284 AGATGCTGCTTATAGATGAGGATCTT 59.559 38.462 0.00 0.00 38.30 2.40
2893 2972 6.555812 ACGAAAGTAAAGTTCCAGGATTTC 57.444 37.500 0.00 0.00 46.88 2.17
2952 3031 8.823220 ACAATTGGCCTACATTATAGAGTTTT 57.177 30.769 10.83 0.00 0.00 2.43
2968 3047 5.246307 AGAGTTTTGACCTATGGTGTTAGC 58.754 41.667 0.00 0.00 35.25 3.09
2969 3048 5.013183 AGAGTTTTGACCTATGGTGTTAGCT 59.987 40.000 0.00 0.00 35.25 3.32
2971 3050 6.775708 AGTTTTGACCTATGGTGTTAGCTTA 58.224 36.000 0.00 0.00 35.25 3.09
2972 3051 6.879458 AGTTTTGACCTATGGTGTTAGCTTAG 59.121 38.462 0.00 0.00 35.25 2.18
2974 3053 6.808321 TTGACCTATGGTGTTAGCTTAGAT 57.192 37.500 0.00 0.00 35.25 1.98
2975 3054 7.907841 TTGACCTATGGTGTTAGCTTAGATA 57.092 36.000 0.00 0.00 35.25 1.98
3036 3124 5.357032 GCATTATAACTAGCAAACACCTGGT 59.643 40.000 0.00 0.00 0.00 4.00
3043 3131 0.312102 GCAAACACCTGGTCTCTTGC 59.688 55.000 16.70 16.70 34.63 4.01
3058 3146 4.021894 GTCTCTTGCCTGTTCAGAGTTCTA 60.022 45.833 1.00 0.00 0.00 2.10
3060 3148 4.825422 TCTTGCCTGTTCAGAGTTCTATG 58.175 43.478 1.00 0.00 0.00 2.23
3065 3153 5.425217 TGCCTGTTCAGAGTTCTATGGAATA 59.575 40.000 0.00 0.00 33.71 1.75
3068 3156 7.687837 GCCTGTTCAGAGTTCTATGGAATATCA 60.688 40.741 0.00 0.00 33.71 2.15
3092 3180 5.643421 ATATCTTCTTGAAGCTGGGTGAT 57.357 39.130 5.56 0.00 0.00 3.06
3107 3195 2.092914 GGGTGATAGTCAAGGACCTTGG 60.093 54.545 29.76 14.28 41.33 3.61
3150 3238 7.170965 TCTCTGGTGCTTGAATCTTATTTCTT 58.829 34.615 0.00 0.00 0.00 2.52
3151 3239 7.335422 TCTCTGGTGCTTGAATCTTATTTCTTC 59.665 37.037 0.00 0.00 0.00 2.87
3158 3246 6.963805 GCTTGAATCTTATTTCTTCGGTTCAG 59.036 38.462 0.00 0.00 0.00 3.02
3209 3301 5.652452 GTGCTATTCCAGGGTATGTTCTTTT 59.348 40.000 0.00 0.00 0.00 2.27
3212 3304 6.603599 GCTATTCCAGGGTATGTTCTTTTTCT 59.396 38.462 0.00 0.00 0.00 2.52
3221 3313 7.342026 AGGGTATGTTCTTTTTCTGTTTGAAGT 59.658 33.333 0.00 0.00 35.89 3.01
3241 3333 7.804614 GAAGTCTACTTCTCTGTATGTGTTG 57.195 40.000 14.26 0.00 46.59 3.33
3267 3359 6.646240 GCTCCTTTGTTTATTGCTTGATGAAA 59.354 34.615 0.00 0.00 0.00 2.69
3270 3362 9.859427 TCCTTTGTTTATTGCTTGATGAAATAG 57.141 29.630 0.00 0.00 28.52 1.73
3271 3363 9.643693 CCTTTGTTTATTGCTTGATGAAATAGT 57.356 29.630 0.00 0.00 28.52 2.12
3273 3365 8.984891 TTGTTTATTGCTTGATGAAATAGTGG 57.015 30.769 0.00 0.00 28.52 4.00
3274 3366 7.546358 TGTTTATTGCTTGATGAAATAGTGGG 58.454 34.615 0.00 0.00 28.52 4.61
3275 3367 7.395772 TGTTTATTGCTTGATGAAATAGTGGGA 59.604 33.333 0.00 0.00 28.52 4.37
3276 3368 7.953005 TTATTGCTTGATGAAATAGTGGGAA 57.047 32.000 0.00 0.00 28.52 3.97
3277 3369 8.537728 TTATTGCTTGATGAAATAGTGGGAAT 57.462 30.769 0.00 0.00 28.52 3.01
3278 3370 6.855763 TTGCTTGATGAAATAGTGGGAATT 57.144 33.333 0.00 0.00 0.00 2.17
3282 3374 7.068593 TGCTTGATGAAATAGTGGGAATTTAGG 59.931 37.037 0.00 0.00 0.00 2.69
3312 3404 6.985188 TCATATGTTCTGTACCTTTTCAGC 57.015 37.500 1.90 0.00 0.00 4.26
3320 3412 7.934665 TGTTCTGTACCTTTTCAGCTATGTAAA 59.065 33.333 0.00 0.00 0.00 2.01
3324 3416 8.630054 TGTACCTTTTCAGCTATGTAAATTGT 57.370 30.769 0.00 0.00 0.00 2.71
3328 3420 7.668052 ACCTTTTCAGCTATGTAAATTGTGGTA 59.332 33.333 0.00 0.00 26.60 3.25
3329 3421 8.519526 CCTTTTCAGCTATGTAAATTGTGGTAA 58.480 33.333 0.00 0.00 0.00 2.85
3332 3424 9.853555 TTTCAGCTATGTAAATTGTGGTAATTG 57.146 29.630 0.00 0.00 0.00 2.32
3391 3551 3.550436 GGATGAAACGTATCTCGACCTCC 60.550 52.174 0.00 0.00 42.86 4.30
3437 3598 6.223852 ACTCCATGGTAATCAAGTTATAGCG 58.776 40.000 12.58 0.00 0.00 4.26
3443 3604 6.046593 TGGTAATCAAGTTATAGCGTGGAAG 58.953 40.000 2.95 0.00 0.00 3.46
3465 3626 5.959652 GAGATTTCTCTAGGCTTTCGTTC 57.040 43.478 0.00 0.00 39.81 3.95
3466 3627 5.407407 AGATTTCTCTAGGCTTTCGTTCA 57.593 39.130 0.00 0.00 0.00 3.18
3479 3640 5.383130 GCTTTCGTTCATTAACTTCAGGTC 58.617 41.667 0.00 0.00 33.15 3.85
3499 3675 9.562408 TCAGGTCAAGAGTATATAGAAGTAGTG 57.438 37.037 0.00 0.00 0.00 2.74
3515 3691 6.778559 AGAAGTAGTGGAGAACTTAGACTTGT 59.221 38.462 0.00 0.00 36.02 3.16
3525 3701 5.696724 AGAACTTAGACTTGTTGAACCATCG 59.303 40.000 0.00 0.00 0.00 3.84
3529 3705 6.317893 ACTTAGACTTGTTGAACCATCGTTTT 59.682 34.615 0.00 0.00 30.30 2.43
3541 3717 2.734606 CCATCGTTTTAGCGAACAGTGA 59.265 45.455 0.00 0.00 44.38 3.41
3569 3746 1.131638 TCAGGTAGGGCATCATGGTC 58.868 55.000 0.00 0.00 0.00 4.02
3598 3775 4.820894 AAATCTACGTTAGGCCTTCTGT 57.179 40.909 12.58 9.81 0.00 3.41
3599 3776 5.927281 AAATCTACGTTAGGCCTTCTGTA 57.073 39.130 12.58 10.50 0.00 2.74
3608 3785 6.370718 ACGTTAGGCCTTCTGTAGTTAATTTG 59.629 38.462 12.58 0.00 0.00 2.32
3620 3797 8.328758 TCTGTAGTTAATTTGATCCATGGACTT 58.671 33.333 18.99 0.80 0.00 3.01
3621 3798 8.279970 TGTAGTTAATTTGATCCATGGACTTG 57.720 34.615 18.99 0.00 0.00 3.16
3640 3817 6.294176 GGACTTGAATTTACTGCAGTGTTCAT 60.294 38.462 28.77 21.08 30.94 2.57
3651 3828 0.235665 AGTGTTCATGCAACTTCGCG 59.764 50.000 0.00 0.00 35.79 5.87
3661 3838 3.805823 TGCAACTTCGCGAGTAAATTTC 58.194 40.909 9.59 0.00 37.72 2.17
3662 3839 3.161306 GCAACTTCGCGAGTAAATTTCC 58.839 45.455 9.59 0.00 37.72 3.13
3663 3840 3.364565 GCAACTTCGCGAGTAAATTTCCA 60.365 43.478 9.59 0.00 37.72 3.53
3682 3859 4.141287 TCCATCTTGGATTGTTGAACGTT 58.859 39.130 0.00 0.00 42.67 3.99
3685 3862 6.093495 TCCATCTTGGATTGTTGAACGTTATC 59.907 38.462 0.00 0.00 42.67 1.75
3695 3872 4.982295 TGTTGAACGTTATCTGTGACTCAG 59.018 41.667 0.00 0.00 44.85 3.35
3726 3906 3.221771 TGTTACAGTTGCAGGCAAGAAT 58.778 40.909 6.99 0.00 36.52 2.40
3740 3920 3.588955 GCAAGAATTTTGGGATCACACC 58.411 45.455 0.00 0.00 0.00 4.16
3752 3932 0.542702 ATCACACCCCCAAAAGGCAG 60.543 55.000 0.00 0.00 0.00 4.85
3769 3952 1.270518 GCAGTCCTTCTGAACTCTGCA 60.271 52.381 21.09 0.00 46.27 4.41
3771 3954 2.805099 CAGTCCTTCTGAACTCTGCAAC 59.195 50.000 0.00 0.00 46.27 4.17
3775 3958 2.989840 CCTTCTGAACTCTGCAACGTAG 59.010 50.000 0.00 0.00 0.00 3.51
3776 3959 2.724977 TCTGAACTCTGCAACGTAGG 57.275 50.000 0.00 0.00 0.00 3.18
3777 3960 2.235891 TCTGAACTCTGCAACGTAGGA 58.764 47.619 0.00 0.00 0.00 2.94
3787 3970 4.460034 TCTGCAACGTAGGAGTATGTACAA 59.540 41.667 0.00 0.00 0.00 2.41
3789 3972 5.539979 TGCAACGTAGGAGTATGTACAAAA 58.460 37.500 0.00 0.00 0.00 2.44
3790 3973 5.990386 TGCAACGTAGGAGTATGTACAAAAA 59.010 36.000 0.00 0.00 0.00 1.94
3828 4011 2.331132 GCAGTGGCTCAGAAGGTGC 61.331 63.158 0.00 0.00 36.96 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
449 469 4.824479 TTATGACTGCTTCATGGACTGA 57.176 40.909 10.63 0.00 45.22 3.41
612 634 9.238368 TCCATTTGAAAATAGTTCCGATAACTT 57.762 29.630 8.18 0.00 0.00 2.66
742 765 8.367156 ACAAACTACACAAGCAATTTCCAATAT 58.633 29.630 0.00 0.00 0.00 1.28
765 793 2.551887 ACACGCATATTCAACAGCACAA 59.448 40.909 0.00 0.00 0.00 3.33
788 816 9.927668 CAGGTTTCAATCCACTTGTAAAATATT 57.072 29.630 0.00 0.00 36.20 1.28
829 899 7.255001 GGTGGTATTTTCTATCCGGTTGTAATG 60.255 40.741 0.00 0.00 0.00 1.90
944 1014 6.299141 TGGAATGATCTATGTTTAGGCCTTC 58.701 40.000 12.58 0.00 0.00 3.46
946 1016 5.912149 TGGAATGATCTATGTTTAGGCCT 57.088 39.130 11.78 11.78 0.00 5.19
947 1017 6.716628 TGAATGGAATGATCTATGTTTAGGCC 59.283 38.462 0.00 0.00 0.00 5.19
948 1018 7.229306 TGTGAATGGAATGATCTATGTTTAGGC 59.771 37.037 0.00 0.00 0.00 3.93
949 1019 8.681486 TGTGAATGGAATGATCTATGTTTAGG 57.319 34.615 0.00 0.00 0.00 2.69
950 1020 9.551734 TCTGTGAATGGAATGATCTATGTTTAG 57.448 33.333 0.00 0.00 0.00 1.85
951 1021 9.330063 GTCTGTGAATGGAATGATCTATGTTTA 57.670 33.333 0.00 0.00 0.00 2.01
952 1022 8.051535 AGTCTGTGAATGGAATGATCTATGTTT 58.948 33.333 0.00 0.00 0.00 2.83
953 1023 7.571919 AGTCTGTGAATGGAATGATCTATGTT 58.428 34.615 0.00 0.00 0.00 2.71
954 1024 7.070946 AGAGTCTGTGAATGGAATGATCTATGT 59.929 37.037 0.00 0.00 0.00 2.29
955 1025 7.385478 CAGAGTCTGTGAATGGAATGATCTATG 59.615 40.741 12.28 0.00 0.00 2.23
956 1026 7.443477 CAGAGTCTGTGAATGGAATGATCTAT 58.557 38.462 12.28 0.00 0.00 1.98
957 1027 6.183360 CCAGAGTCTGTGAATGGAATGATCTA 60.183 42.308 18.74 0.00 32.55 1.98
958 1028 5.396548 CCAGAGTCTGTGAATGGAATGATCT 60.397 44.000 18.74 0.00 32.55 2.75
959 1029 4.815308 CCAGAGTCTGTGAATGGAATGATC 59.185 45.833 18.74 0.00 32.55 2.92
960 1030 4.472470 TCCAGAGTCTGTGAATGGAATGAT 59.528 41.667 18.74 0.00 37.12 2.45
961 1031 3.840078 TCCAGAGTCTGTGAATGGAATGA 59.160 43.478 18.74 2.18 37.12 2.57
962 1032 4.212143 TCCAGAGTCTGTGAATGGAATG 57.788 45.455 18.74 0.00 37.12 2.67
963 1033 5.045359 TGAATCCAGAGTCTGTGAATGGAAT 60.045 40.000 18.74 1.87 42.98 3.01
964 1034 4.286808 TGAATCCAGAGTCTGTGAATGGAA 59.713 41.667 18.74 0.00 42.98 3.53
965 1035 3.840078 TGAATCCAGAGTCTGTGAATGGA 59.160 43.478 18.74 9.05 43.82 3.41
966 1036 3.937706 GTGAATCCAGAGTCTGTGAATGG 59.062 47.826 18.74 3.47 0.00 3.16
967 1037 4.572909 TGTGAATCCAGAGTCTGTGAATG 58.427 43.478 18.74 3.33 0.00 2.67
968 1038 4.897509 TGTGAATCCAGAGTCTGTGAAT 57.102 40.909 18.74 8.82 0.00 2.57
969 1039 4.529769 AGATGTGAATCCAGAGTCTGTGAA 59.470 41.667 18.74 4.63 0.00 3.18
970 1040 4.092279 AGATGTGAATCCAGAGTCTGTGA 58.908 43.478 18.74 15.02 0.00 3.58
971 1041 4.468765 AGATGTGAATCCAGAGTCTGTG 57.531 45.455 18.74 10.34 0.00 3.66
972 1042 4.776837 AGAAGATGTGAATCCAGAGTCTGT 59.223 41.667 18.74 0.02 0.00 3.41
973 1043 5.341872 AGAAGATGTGAATCCAGAGTCTG 57.658 43.478 13.56 13.56 0.00 3.51
974 1044 6.406849 GCTTAGAAGATGTGAATCCAGAGTCT 60.407 42.308 0.00 0.00 0.00 3.24
975 1045 5.752955 GCTTAGAAGATGTGAATCCAGAGTC 59.247 44.000 0.00 0.00 0.00 3.36
976 1046 5.188555 TGCTTAGAAGATGTGAATCCAGAGT 59.811 40.000 0.00 0.00 0.00 3.24
977 1047 5.668471 TGCTTAGAAGATGTGAATCCAGAG 58.332 41.667 0.00 0.00 0.00 3.35
978 1048 5.682234 TGCTTAGAAGATGTGAATCCAGA 57.318 39.130 0.00 0.00 0.00 3.86
979 1049 5.238868 CCATGCTTAGAAGATGTGAATCCAG 59.761 44.000 0.00 0.00 0.00 3.86
980 1050 5.128205 CCATGCTTAGAAGATGTGAATCCA 58.872 41.667 0.00 0.00 0.00 3.41
981 1051 4.023365 GCCATGCTTAGAAGATGTGAATCC 60.023 45.833 0.00 0.00 0.00 3.01
982 1052 4.577693 TGCCATGCTTAGAAGATGTGAATC 59.422 41.667 0.00 0.00 0.00 2.52
983 1053 4.529897 TGCCATGCTTAGAAGATGTGAAT 58.470 39.130 0.00 0.00 0.00 2.57
984 1054 3.943381 CTGCCATGCTTAGAAGATGTGAA 59.057 43.478 0.00 0.00 0.00 3.18
985 1055 3.538591 CTGCCATGCTTAGAAGATGTGA 58.461 45.455 0.00 0.00 0.00 3.58
986 1056 2.617308 CCTGCCATGCTTAGAAGATGTG 59.383 50.000 0.00 0.00 0.00 3.21
987 1057 2.240667 ACCTGCCATGCTTAGAAGATGT 59.759 45.455 0.00 0.00 0.00 3.06
988 1058 2.877168 GACCTGCCATGCTTAGAAGATG 59.123 50.000 0.00 0.00 0.00 2.90
989 1059 2.484417 CGACCTGCCATGCTTAGAAGAT 60.484 50.000 0.00 0.00 0.00 2.40
990 1060 1.134699 CGACCTGCCATGCTTAGAAGA 60.135 52.381 0.00 0.00 0.00 2.87
991 1061 1.293924 CGACCTGCCATGCTTAGAAG 58.706 55.000 0.00 0.00 0.00 2.85
1046 1116 0.250513 GGAGAATGTGGAGGCGAGTT 59.749 55.000 0.00 0.00 0.00 3.01
1047 1117 0.616111 AGGAGAATGTGGAGGCGAGT 60.616 55.000 0.00 0.00 0.00 4.18
1059 1129 1.522569 GGCGCTGTGGTAGGAGAAT 59.477 57.895 7.64 0.00 0.00 2.40
1286 1365 1.746517 GTCCAGGTGACCACGTTCT 59.253 57.895 3.63 0.00 38.09 3.01
1542 1621 0.449388 CGGGCATTCTCTCAAACAGC 59.551 55.000 0.00 0.00 0.00 4.40
1623 1702 3.226429 AAACAGCGCTCGAGCCTCA 62.226 57.895 30.66 0.00 37.91 3.86
1713 1792 2.270352 ACAAATCAAGGGCTTCGTCA 57.730 45.000 0.00 0.00 0.00 4.35
1722 1801 5.987347 GGGCATATTCATGAACAAATCAAGG 59.013 40.000 11.07 0.00 42.54 3.61
1773 1852 5.880164 TCTGGATAAAACCGGTGATCATA 57.120 39.130 8.52 4.39 37.55 2.15
2075 2154 7.117236 CACATTTGGCATATAAATTCATGAGGC 59.883 37.037 0.00 0.00 0.00 4.70
2076 2155 7.601130 CCACATTTGGCATATAAATTCATGAGG 59.399 37.037 0.00 0.00 35.56 3.86
2112 2191 1.754226 TCAAACACCTTCCTTGCCAAC 59.246 47.619 0.00 0.00 0.00 3.77
2348 2427 3.803082 CCCGCACTGCAATGGACG 61.803 66.667 0.00 0.00 0.00 4.79
2373 2452 5.873712 ACAGAGATCAATCAAGCAAGTGTAG 59.126 40.000 0.00 0.00 0.00 2.74
2409 2488 3.411446 TCTTTTGGCATCATCAAGTCGT 58.589 40.909 0.00 0.00 0.00 4.34
2517 2596 2.016318 CTTGCTGCCAAATCACCGATA 58.984 47.619 0.00 0.00 0.00 2.92
2556 2635 5.186198 GTGTAAGTTCCAGCATTATCAGGT 58.814 41.667 0.00 0.00 0.00 4.00
2580 2659 7.678218 GCAGAAGCATAAATGTTAGACAAGAGG 60.678 40.741 0.00 0.00 41.58 3.69
2667 2746 0.253044 TCCAACTACATCCTGGCTGC 59.747 55.000 0.00 0.00 0.00 5.25
2706 2785 4.311606 TGTCACGTGCTACAAATACATGT 58.688 39.130 11.67 2.69 37.32 3.21
2739 2818 6.416455 GCAGACTATAAATCAACTCAGACTCG 59.584 42.308 0.00 0.00 0.00 4.18
2817 2896 6.224665 AGATCCTCATCTATAAGCAGCATC 57.775 41.667 0.00 0.00 37.63 3.91
2822 2901 5.840693 TCCACAAGATCCTCATCTATAAGCA 59.159 40.000 0.00 0.00 38.55 3.91
2893 2972 1.135575 GCAAAATGCTTCCCTCTGACG 60.136 52.381 0.00 0.00 40.96 4.35
2924 3003 7.573710 ACTCTATAATGTAGGCCAATTGTCAA 58.426 34.615 5.01 0.00 0.00 3.18
2943 3022 7.048512 GCTAACACCATAGGTCAAAACTCTAT 58.951 38.462 0.00 0.00 31.02 1.98
2952 3031 7.728532 TCATATCTAAGCTAACACCATAGGTCA 59.271 37.037 0.00 0.00 32.69 4.02
2968 3047 4.421131 AGCCTGGGGTACTCATATCTAAG 58.579 47.826 0.00 0.00 0.00 2.18
2969 3048 4.487282 AGCCTGGGGTACTCATATCTAA 57.513 45.455 0.00 0.00 0.00 2.10
2971 3050 4.140663 ACTTAGCCTGGGGTACTCATATCT 60.141 45.833 0.00 0.00 0.00 1.98
2972 3051 4.161102 ACTTAGCCTGGGGTACTCATATC 58.839 47.826 0.00 0.00 0.00 1.63
2974 3053 3.700863 ACTTAGCCTGGGGTACTCATA 57.299 47.619 0.00 0.00 0.00 2.15
2975 3054 2.505819 CAACTTAGCCTGGGGTACTCAT 59.494 50.000 0.00 0.00 0.00 2.90
3036 3124 2.968574 AGAACTCTGAACAGGCAAGAGA 59.031 45.455 5.95 0.00 0.00 3.10
3043 3131 7.730084 TGATATTCCATAGAACTCTGAACAGG 58.270 38.462 1.93 0.00 33.97 4.00
3065 3153 6.320672 CACCCAGCTTCAAGAAGATATTTGAT 59.679 38.462 13.70 0.00 40.79 2.57
3068 3156 5.819991 TCACCCAGCTTCAAGAAGATATTT 58.180 37.500 13.70 0.00 40.79 1.40
3074 3162 4.187694 GACTATCACCCAGCTTCAAGAAG 58.812 47.826 5.46 5.46 41.24 2.85
3092 3180 3.833070 GACTTCTCCAAGGTCCTTGACTA 59.167 47.826 29.91 15.10 43.42 2.59
3107 3195 6.071051 ACCAGAGATAAAGGTCAAGACTTCTC 60.071 42.308 0.00 5.30 0.00 2.87
3221 3313 4.772624 AGCCAACACATACAGAGAAGTAGA 59.227 41.667 0.00 0.00 0.00 2.59
3224 3316 3.307059 GGAGCCAACACATACAGAGAAGT 60.307 47.826 0.00 0.00 0.00 3.01
3241 3333 4.519540 TCAAGCAATAAACAAAGGAGCC 57.480 40.909 0.00 0.00 0.00 4.70
3368 3528 2.361438 AGGTCGAGATACGTTTCATCCC 59.639 50.000 8.74 3.01 43.13 3.85
3369 3529 3.550436 GGAGGTCGAGATACGTTTCATCC 60.550 52.174 8.74 5.09 43.13 3.51
3373 3533 5.468072 TGTATAGGAGGTCGAGATACGTTTC 59.532 44.000 0.00 0.00 43.13 2.78
3378 3538 6.094061 GCAAATGTATAGGAGGTCGAGATAC 58.906 44.000 0.00 0.00 0.00 2.24
3381 3541 3.958147 TGCAAATGTATAGGAGGTCGAGA 59.042 43.478 0.00 0.00 0.00 4.04
3384 3544 3.187227 GCATGCAAATGTATAGGAGGTCG 59.813 47.826 14.21 0.00 0.00 4.79
3391 3551 7.645340 GGAGTTACAAAGCATGCAAATGTATAG 59.355 37.037 21.98 1.42 0.00 1.31
3443 3604 5.411781 TGAACGAAAGCCTAGAGAAATCTC 58.588 41.667 2.10 2.10 43.17 2.75
3456 3617 5.049680 TGACCTGAAGTTAATGAACGAAAGC 60.050 40.000 0.00 0.00 40.76 3.51
3498 3674 5.104693 TGGTTCAACAAGTCTAAGTTCTCCA 60.105 40.000 0.00 0.00 0.00 3.86
3499 3675 5.365619 TGGTTCAACAAGTCTAAGTTCTCC 58.634 41.667 0.00 0.00 0.00 3.71
3505 3681 5.924475 AACGATGGTTCAACAAGTCTAAG 57.076 39.130 0.00 0.00 0.00 2.18
3506 3682 6.687081 AAAACGATGGTTCAACAAGTCTAA 57.313 33.333 0.00 0.00 34.62 2.10
3511 3687 3.906008 CGCTAAAACGATGGTTCAACAAG 59.094 43.478 0.00 0.00 34.62 3.16
3513 3689 3.132160 TCGCTAAAACGATGGTTCAACA 58.868 40.909 0.00 0.00 37.09 3.33
3515 3691 3.560481 TGTTCGCTAAAACGATGGTTCAA 59.440 39.130 0.00 0.00 42.54 2.69
3525 3701 1.197036 GGGCTCACTGTTCGCTAAAAC 59.803 52.381 0.00 0.00 0.00 2.43
3529 3705 1.591703 CAGGGCTCACTGTTCGCTA 59.408 57.895 0.00 0.00 33.81 4.26
3579 3756 4.534797 ACTACAGAAGGCCTAACGTAGAT 58.465 43.478 28.79 16.88 32.56 1.98
3584 3761 6.592607 TCAAATTAACTACAGAAGGCCTAACG 59.407 38.462 5.16 0.00 0.00 3.18
3585 3762 7.916914 TCAAATTAACTACAGAAGGCCTAAC 57.083 36.000 5.16 3.23 0.00 2.34
3586 3763 7.773690 GGATCAAATTAACTACAGAAGGCCTAA 59.226 37.037 5.16 0.00 0.00 2.69
3587 3764 7.092623 TGGATCAAATTAACTACAGAAGGCCTA 60.093 37.037 5.16 0.00 0.00 3.93
3588 3765 6.122964 GGATCAAATTAACTACAGAAGGCCT 58.877 40.000 0.00 0.00 0.00 5.19
3589 3766 5.885912 TGGATCAAATTAACTACAGAAGGCC 59.114 40.000 0.00 0.00 0.00 5.19
3590 3767 7.420800 CATGGATCAAATTAACTACAGAAGGC 58.579 38.462 0.00 0.00 0.00 4.35
3591 3768 7.775093 TCCATGGATCAAATTAACTACAGAAGG 59.225 37.037 11.44 0.00 0.00 3.46
3592 3769 8.616076 GTCCATGGATCAAATTAACTACAGAAG 58.384 37.037 19.62 0.00 0.00 2.85
3593 3770 8.328758 AGTCCATGGATCAAATTAACTACAGAA 58.671 33.333 19.62 0.00 0.00 3.02
3594 3771 7.861629 AGTCCATGGATCAAATTAACTACAGA 58.138 34.615 19.62 0.00 0.00 3.41
3595 3772 8.400947 CAAGTCCATGGATCAAATTAACTACAG 58.599 37.037 19.62 0.00 0.00 2.74
3596 3773 8.106462 TCAAGTCCATGGATCAAATTAACTACA 58.894 33.333 19.62 0.00 0.00 2.74
3597 3774 8.506168 TCAAGTCCATGGATCAAATTAACTAC 57.494 34.615 19.62 0.00 0.00 2.73
3598 3775 9.699410 ATTCAAGTCCATGGATCAAATTAACTA 57.301 29.630 19.62 0.00 0.00 2.24
3599 3776 8.599624 ATTCAAGTCCATGGATCAAATTAACT 57.400 30.769 19.62 4.27 0.00 2.24
3608 3785 5.357878 TGCAGTAAATTCAAGTCCATGGATC 59.642 40.000 19.62 11.77 0.00 3.36
3620 3797 4.277921 TGCATGAACACTGCAGTAAATTCA 59.722 37.500 28.50 28.50 44.30 2.57
3621 3798 4.797471 TGCATGAACACTGCAGTAAATTC 58.203 39.130 21.20 21.72 44.30 2.17
3640 3817 3.364565 GGAAATTTACTCGCGAAGTTGCA 60.365 43.478 11.33 0.00 39.55 4.08
3645 3822 5.258622 CAAGATGGAAATTTACTCGCGAAG 58.741 41.667 11.33 7.16 0.00 3.79
3648 3825 3.621268 TCCAAGATGGAAATTTACTCGCG 59.379 43.478 0.00 0.00 45.00 5.87
3661 3838 4.503741 AACGTTCAACAATCCAAGATGG 57.496 40.909 0.00 0.00 39.43 3.51
3662 3839 6.963242 CAGATAACGTTCAACAATCCAAGATG 59.037 38.462 2.82 0.00 0.00 2.90
3663 3840 6.655003 ACAGATAACGTTCAACAATCCAAGAT 59.345 34.615 2.82 0.00 0.00 2.40
3675 3852 4.262036 AAGCTGAGTCACAGATAACGTTCA 60.262 41.667 2.82 0.00 44.93 3.18
3679 3856 2.346847 GCAAGCTGAGTCACAGATAACG 59.653 50.000 0.95 0.00 44.93 3.18
3682 3859 5.604758 AATAGCAAGCTGAGTCACAGATA 57.395 39.130 4.53 0.00 44.93 1.98
3695 3872 4.545610 TGCAACTGTAACAAATAGCAAGC 58.454 39.130 0.00 0.00 0.00 4.01
3752 3932 1.795286 CGTTGCAGAGTTCAGAAGGAC 59.205 52.381 0.00 0.00 0.00 3.85
3758 3941 2.029828 ACTCCTACGTTGCAGAGTTCAG 60.030 50.000 0.00 0.00 36.16 3.02
3828 4011 0.904394 CCCATTCCCAACACAAGGGG 60.904 60.000 0.00 0.00 46.77 4.79
3830 4013 1.549203 CTCCCATTCCCAACACAAGG 58.451 55.000 0.00 0.00 0.00 3.61
3834 4017 2.291540 TGATTCCTCCCATTCCCAACAC 60.292 50.000 0.00 0.00 0.00 3.32
3837 4020 1.570501 CCTGATTCCTCCCATTCCCAA 59.429 52.381 0.00 0.00 0.00 4.12


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.